Tandem mass spectrometers (MS/MS) are used for elucidation of the structure of analyte molecules. In a typical MS/MS system, a parent, or “precursor”, molecule is ionized and then selected out of an analyte sample using a first stage mass analyzer. The precursor ions are then transported to a region in which they are subjected to one or more activating influences that excite the ions, which induces fragmentation of the precursor ions into product ions and neutral fragments. The product ions can then be analyzed in the second stage mass analyzer, and the resulting mass spectrum of the product ions can reveal a great deal of information about the structure of the precursor molecule.
Product ions will be observed in the mass spectrum if they are generated by fragmentation at a high rate compared to the length of time that a precursor ion travels through the activation region. Regardless of the activation technique employed, the rate at which fragmentation occurs, referred to as the dissociation rate, is found to depend on the internal energy distribution of the precursor ions. FIG. 1 shows an expected distribution of internal energies of precursor ions in a mass spectrometer instrument. As can be discerned, the precursor ions at higher internal energies have a relatively higher dissociation rate, and are denoted as “unstable”.
While FIG. 1 indicates that only a small portion of the total population of precursor ions have high internal energies and dissociation rates, the relative portion of unstable ions is not necessarily static since activation methods can be employed to increase the total internal energy of the ions, in effect shifting the entire curve to the right. There are a number of activation methods available, and one of the more commonly employed techniques is collision-induced dissociation (“CID”) (also referred to as collision-activated dissociation (CAD)) in which the precursor ions are subjected to collisions with atoms of neutral particles in a chamber situated between the two mass analyzer stages. The neutral is typically an inert, noble gas such as helium or argon which does not interact chemically with the precursor ions during collisions.
When a precursor ion undergoes an inelastic collision with a neutral particle, part of the kinetic energy of the precursor ion is converted into internal energy, which, at low kinetic energies, usually causes excitation of vibrational states. However, the amount of kinetic energy that can be converted to internal energy is highly dependent on the relative masses of the ion and the neutral according to the formula:Econv=N/(mp+N)×KE  (1)where Econv is the maximum energy available for conversion, KE is the kinetic energy of the precursor ion and N and mp represent the masses of the neutral particle and the precursor ion, respectively. From equation (1), it can be seen that the total energy available for conversion per collision is proportional to the kinetic energy of the ion, that conversion efficiency can be increased by using high mass neutral species, and that the conversion efficiency decreases as the mass of the precursor ion of interest increases.
Ions produced in atmospheric ion sources typically undergo a supersonic expansion as they flow downstream into low pressure regions of the mass spectrometer. The supersonic expansion cools the ions, and their internal energy drops to a very “cold” state even though the kinetic energy of these ions may be high. As the ions are subjected to collisions, the kinetic energy of the collisions gradually thermalizes the ions, raising their internal temperature, and spreading energy among their various internal vibrational modes. As the internal temperature of the ions rise, incipient instabilities in the precursor ions can emerge as certain vibrational modes acquire more energy than they can hold.
Configurations for tandem mass spectrometers at present are often inefficient in producing product ions partly because precursor ions arrive at the collision cells of these instruments with insufficient internal energy due to the cooling effect of the supersonic expansion. Therefore, there exists a need for a method and apparatus for ensuring that the precursor ions are thermalized by the time that fragmentation of the ions is designed to occur. In addition, there exists a need to control the precursor ion activation process so as to enable a variation of the fragmentation patterns by selectively adjusting the internal energy levels of the precursor ions (with their corresponding vibrational modes and probable instabilities) as they enter the fragmentation region.